1- The DiffBind vignette (section 8.2 - Deriving consensus peaksets) states
When performing an overlap analysis, it is often the case that the overlap criteria are set stringently in order to lower noise and drive down false positives. It is less clear that limiting the potential binding sites in this way is appropriate when focusing on affinity data, as the differential binding analysis method will identify only sites that are significantly differentially bound, even if operating on peaksets that include incorrectly identified sites.
Does not it makes sense then to be permissive when setting consensus peaksets for affinity analysis? Practically speaking, this means taking all peaks which appear in at least one sample is a good default strategy (unless there is a reason not to).
2- If one decides she wants to be nevertheless more stringent, I think that there is a large conceptual difference between peaks that are shared between two replicates of the same condition (but not across the conditions), and two peaks that are shared between two samples of different conditions (but not across the replicates within the conditions).
In the first case, the fact that the peaks exist for both replicates brings greater confidence in the peak called. In the other case however, the fact that the same peak exists in two conditions does not suggest a greater confidence that there is truly differential affinity at that site. If two peaks exist across two different conditions (but not within the conditions), this suggests quite the opposite - that this is not an area with differential affinity. That is because it (a) exists in both of the conditions which lessens the plausibility of it being differential, and (b) does not exist in the replicates of each condition, which it increases the possibility of it being random.
Practically speaking, this means that a good default way to perform a stringent analysis is to define a peakset (for differential affinity) as peaks that exist in at least two replicates of a condition.
Do you think these points are valid?